7YPL | pdb_00007ypl

Crystal structure of fibronectin type III domain variant, a VEGFR2-specific antagonist

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Li2SO4 0.1M CHES pH 9.5 0.7M K/Na tartrate

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.791	α = 90
b = 68.791	β = 90
c = 68.799	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RAYONIX MX300-HS		2016-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.0000	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.63	30	100	0.895	32.7	10		12563

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.69			0.973

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4LXO	1.63	29.792	12528	631	99.936	0.179	0.1774	0.19	0.2133	0.22	18.583

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.098	0.049		0.098		-0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.614
r_dihedral_angle_3_deg	13.62
r_dihedral_angle_4_deg	12.757
r_dihedral_angle_1_deg	7.774
r_lrange_it	5.526
r_lrange_other	5.468
r_scangle_it	3.918
r_scangle_other	3.617
r_mcangle_it	2.98
r_mcangle_other	2.978
r_scbond_it	2.496
r_scbond_other	2.313
r_mcbond_other	1.824
r_mcbond_it	1.823
r_angle_refined_deg	1.5
r_angle_other_deg	1.394
r_nbd_other	0.272
r_symmetry_nbd_refined	0.24
r_symmetry_nbd_other	0.188
r_symmetry_xyhbond_nbd_refined	0.172
r_nbd_refined	0.171
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.106
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.073
r_xyhbond_nbd_other	0.06
r_gen_planes_refined	0.016
r_bond_refined_d	0.01
r_gen_planes_other	0.003
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	799
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing